Junk DNA munged

Salvador seems to have successfully hijacked the early embryonic mutations thread and turned it into a discussion of junk DNA. So I thought I’d share my thoughts on the subject of junk DNA. Why care?

Various strains of creationism hold that the earth and life started out perfect, then came the fall, and it all went downhill from there. Both young earth and old earth forms can easily accommodate the presence of junk in DNA. So the presence of junk DNA does not mitigate against the creationist position. But what of it’s absence?

Now perhaps it would appear to be nothing short of miraculous if it turned out that the genomes of organisms were mostly or completely functional or otherwise serve some identifiable purpose. But are we even close to being able to demonstrate that such is the case? Anywhere close at all? I think not. Thus the opportunity for much hot air and no end of people willing to spout it. We are far from having a complete understanding so perhaps a wait and see attitude is appropriate.

So arguments over how much DNA is junk and how much isn’t don’t serve much useful purpose in the debate. People aren’t going to be converted. If we simply must talk about junk DNA wouldn’t it be better just to discuss the implications one way or another? If neither side can make predictions that can be falsified what is the point? Ah. Pointless debate. Of course.

Does evolutionary theory predict junk DNA, and if so how much junk does it predict?

What does a phylogeny of junk DNA look like?

If it turned out that the genomes of organisms were mostly or completely functional or otherwise serve some identifiable purpose would evolutionary theory be falsified? My answer to that question is no, evolution would not be shown to be false.

The debate is mostly a waste of time. The irony. 🙂

117 thoughts on “Junk DNA munged

  1. J-Mac:
    Seems to me Larry Moran is pretty open to the idea of a fully functional genome…
    Why is he defending the 10% function then?

    Because that’s what the evidence indicates.

  2. Larry Moran: The term “Darwinist” refers to someone who thinks natural selection is by far the dominant force in evolution.

    With respect to being a designer mimic capable of explaining the vision system, for example. I doubt any serious scientist would think vision systems arose via genetic drift. Darwinists accept genetic drift but theirs is not an argument about variation within a population. Theirs is an argument pertaining to the origins of species- new body plans, new body parts. The history of life vs the journey of an allele or mutation.

    So context is important, Larry.

  3. Adapa: Because that’s what the evidence indicates.

    Funny thing about that.

    Really, place to go to argue function is Larry’s place. Just bring a bucket for your severed limbs.

  4. petrushka: Funny thing about that.

    Really, place to go to argue function is Larry’s place. Just bring a bucket for your severed limbs.

    Larry doesn’t have a mechanism capable of explaining function. He can only try to explain non-function and that isn’t based on knowledge or reasoning.

  5. J-Mac: Seems to me Larry Moran is pretty open to the idea of a fully functional genome…
    Why is he defending the 10% function then?

    He already explained that. Calculations show that with the approximate mutation rates we have, a genome of our size could not be maintained since it would have accumulated too many deleterious mutations long ago. So most of those mutations must happen in “junk”.
    Also, when we look at the genome in more detail, we see that it contains tens of thousands of pseudogenes and dead transposons. Dead transposons are technically pseudogenes too. Pseudogenes are easy to recognize, they look like mutationally degraded genes. For example, a reverse transcriptase gene (including the promoter and enhancer regions), or a DNA polymerase-III gene. But with mutations in it, mutations that would destroy the gene (and it’s enhancer and promoter). Mutations that ruin the transcription factor binding sites. Mutations that cause frameshift mutations in the coding region. Mutations that destroy splicing sites in transcribed regions. Mutations that cause premature stop codons. Mutations that are effectively deletions of large portions of key exons.

    In every imaginable and possible way, they look like dead genes that have accumulated over geological time, due to the combating forces of active transposition and accumulation of deleteriouos mutations. There’s a prediction from genetic load calculations, and then there’s direct observational evidence.

    It’s junk. It looks in every way like junk. Like junk would look if it really was junk. So the case for junk is defended because that’s what the evidence actually really does show. You know how we can recognize a broken, rusty old junk-car from decades of detoriation? It’s the same way with junk DNA. We can simply look at it. They can even find junk DNA in different stages of disrepair, just as you can with junk-cars. Some cars are recently broken, most of the plates are still coated with paint and have very little rust on them. Maybe only a wheel is missing. Other junk-cars have almost disappeared to detoriation. Same with junk-DNA. Some genes are only very recently broken due to mutations. Others have almost become fully erased and there are only scraps left. They’re still “intact enough” that we can compare them to still-functioning genes and see that “this is a piece of a once functional gene”.

    Sure, if you go digging in the junk-car, you might find something that could still work and be put to some use. Maybe there’s still a useful old plastic knob in there, or a piece of wire that hasn’t yet eroded away entirely. But for the most part, that car is junk.

    And we haven’t even talked about genome-size comparisons between different species. Some species have much, much larger genomes than ours. What do we find in them? Even more broken old genes. Looking broken like a slow accumulation of broken genes would be expected to look like: broken due to accumulation of mutations over geological time, and at various stages of disrepair due to how recently they managed to copy themselves and subsequently degraded due to mutation.

    What do we find in species with much, much smaller genomes than ours? Almost no broken genes.

  6. stcordova: Because of Mung referencing my relevant discussion of junkDNA in VJs thread, I’m boycotting this thread other than this comment. I’ll discuss junkDNA elsewhere at TSZ, but not in Mung’s thread.

    LOL.

  7. Mung,

    These point to the argument for common descent, and thus for the “evidence for evolution” being the evidence for common descent.

    Well? Evolution causes change in lineage. From a single ancestor, two separated lineages will both change independently, if evolution happens. So if you find evidence that two lineages are commonly descended, you have found evidence that change-in-lineage has happened – if the two modern forms are no longer identical, but appear commonly descended, then evolution is inferred to have happened, else how did they become different? (I know there are ‘tinkering’ theories, but I see no reason to prefer them to the known processes).

    If you erased one branch from the record, you would no longer have that particular piece of evidence for evolution.

  8. People can just look at things (like cars and DNA) and see junk. It’s pretty obvious.

    I can look at things and see design. It’s also pretty obvious. 🙂

  9. Mung:
    People can just look at things (like cars and DNA) and see junk. It’s pretty obvious.

    I can look at things and see design. It’s also pretty obvious.

    I knew you (or some other IDiot) would do that, I just knew it.

  10. Mung,

    People can just look at things (like cars and DNA) and see junk. It’s pretty obvious.

    I can look at things and see design. It’s also pretty obvious.

    In the case of DNA, if you only have some fragment of the original sequence anyway, or it appears otherwise broken, it is rather hard to see design. One might hope, a la Sal, that there is a cryptic function behind it all anyway, but that is hardly ‘seeing design’ in the way one might point to streamlining or a well-formed beak. It’s more seeking design, because it isn’t obvious.

  11. Mung:
    People can just look at things (like cars and DNA) and see junk. It’s pretty obvious.

    Yes. That really is quite simple. The car in the picture. It looks like junk to me. Key parts of what makes a functional car are either completely missing, or in so bad a state of detoriation they would no longer be able to function. There is no engine and no wheels, for example. For that car to work, it would have to have an engine, and wheels. You can also find pictures of junk-cars that still have an engine, but the engine is broken, or the wheels are broken. You have an expectation of what a functional car looks like, because you know how a car functions.

    It’s exactly like that with genes. For genes to work, they should not have premature stop codons, or missing exons, or ruined splicing sites, or missing or broken promoters. And so on and so forth. In essence, you really can just look at it and see that, yep, this is one broken-fucking-gene.

    There is a grey zone where it’s harder to determine. Again the car analogy can make sense of this. An engine can be damaged, but still remain somewhat functional. Maybe one wheel is missing, or the tire is deflated. Is it a functional car? Maybe. That’s where you plausibly can’t just look at it, you have to try and drive it to see if it’s too broken for proper function. There are gene-versions of that. They might look to be in some state of disrepair that is not “broken enough” to have become entirely nonfunctional. But you’re not quite sure, so you better test it. That’s when you do functional genomics.

    I can look at things and see design. It’s also pretty obvious.

    That’s remarkable. Please teach me.

    I will provide you the Calilasseia-challenge:

    One of these rocks is “designed”, in the sense of being a Palaeolithic stone tool fashioned by human hand. The rest are simply naturally weathered rocks. Can you tell which one is the “designed” rock?

  12. Don’twhackit,

    Don’twhackit,

    This is patently absurd, even for you.

    No one is arguing that if something looks natural, it must be natural, they are arguing that if something looks designed, it must be designed.

    You think there are people who doubt an intelligence could design something that doesn’t look designed?

    Holy shit.

  13. I designed a garden that looks just like a bunch of wild weeds! Can you believe that??

    Dontwhackit would be blown away.

  14. phoodoo:
    You think there are people who doubt an intelligence could design something that doesn’t look designed?

    Which is why ID is unfalsifiable

  15. newton: Which is why ID is unfalsifiable

    Um, it seems you don’t quite get it. Just because things that appeared to be designed, are likely designed, there is no reason WHATSOEVER that the opposite need also be true, that things that don’t look designed aren’t designed.

    Two different issues entirely. Your logic is flawed.

  16. All it takes is a single example to falsify the claim that it is obvious that you can just look at a thing and determine whether it’s designed. In so far as such an example exists, the claim is false.

    There isn’t anything in DNA that looks “obviously” designed to me. Not even likely designed. Simply put, there’s nothing about DNA as found in living organisms that gives away a hint of anything I would associate with being the product of intelligent design.

  17. phoodoo: Um, it seems you don’t quite get it.

    Possibly,

    Just because things that appeared to be designed, are likely designed,

    I agree that some things that look designed are designed because they seem artificial, unnatural. Some looked designed because we observe the processes of design and implementation of the design.

    there is no reason WHATSOEVER that the opposite need also be true, that things that don’t look designed aren’t designed.

    Actually I got that just fine, that is why the design hypothesis is unfalsifiable given an unknown designer with unknown abilties. Unentailed hypotheses are unfalsifiable

    Is my logic still flawed?

  18. It’s moronic to say that ID is unfalsifiable after you have been told how to falsify ID.

    To falsify any given design inference all one has to do is step up and show non-telic processes can account for it. That even applies to Stonehenge- however no one can. That means the design inference for Stonehenge is unfalsifiable which makes it an incontrovertible fact that it was designed.

    It isn’t ID’s fault that there isn’t any way for blind and mindless processes to produce what IDists say is designed.

  19. Allan Miller: In the case of DNA, if you only have some fragment of the original sequence anyway, or it appears otherwise broken, it is rather hard to see design.

    I don’t know about that. Can blind and mindless processes produce DNA at all? That still needs to be demonstrated

  20. Thinks don’t just “look” designed. We have background information that allows us determine some things were designed. We can go to a car factory, find the blueprints, gather all sorts of evidence about how, when and who designed AND BUILT those cars. No one in their right mind would claim that a watch must be designed because it looks like a car, since there’s independent evidence for watch design and construction.

    None of us was ‘built’ like all the designed things we know are built. There’s absolutely nothing in life that suggests it was designed.

    Look how Sal believes celestial bodies were designed too. Mung an other IDists don’t agree, how could they possibly determine who’s right or wrong based on ID paradigms?

    – Sal: The Solar System looks designed!
    – Mung: Not really
    – Sal: It looks designed to me!
    – Mung: Not to me!
    – Sal: It does, just look again!
    – Mung: Heh, hold on. Let me see if I can accommodate that to my version of creationism…

  21. I’ve only read some of the replies so I dont know if anyone else has addressed this but theres one observation that goes a long way to answering Mung’s questions:

    Most vertebrates have a lot of junk DNA (pufferfish are an exception) But bacteria have little or none. The genome of E Coli is mostly wall to wall genes and regulatory sequences. If The Fall explains junk DNA in general how do you explain the fact that ferns have ten times more junk DNA that humans and bacteria have almost none? Scientists explain it in terms of the rate of production of junk DNA vs the rate of removal which are all determined by selection coefficients and population size. Each of these phenomena can be independently studied and verified in many other contexts.

    I think the structure of this argument is similar to many others in which creationist/ID arguments fail. There is some phenomena in nature. Scientists have an evolutionary explanation and IDers have their own explanation in terms of a designer. Very often the ID explanation superficially seems to work , ie. “common design”. Its when you scratch the surface and look at the details that the ID explanation falls apart. There are exceptions and outliers to the phenomena. Evolution can explain them perfectly in terms of natural mechanisms and do further tests to verify those independently. Very often the exceptions are exactly what you’d expect from the operation designerless mechanisms. But the ID explanation, whatever it was usually falls apart under the exceptions.

  22. IDiots often argue that most mutations are deleterious and that’s a problem for evolution. They also argue against jDNA, which means that humans have to deal with ten times more of those mutations in functional DNA. They don’t see a problem with that line of reasoning because they can hardly handle one argument at a time

  23. REW: Evolution can explain them perfectly in terms of natural mechanisms and do further tests to verify those independently.

    Evolutionism cannot account for the organisms who have the alleged junk DNA. So that would be a problem.

  24. Rumraket:
    All it takes is a single example to falsify the claim that it is obvious that you can just look at a thing and determine whether it’s designed. In so far as such an example exists, the claim is false.

    There isn’t anything in DNA that looks “obviously” designed to me. Not even likely designed. Simply put, there’s nothing about DNA as found in living organisms that gives away a hint of anything I would associate with being the product of intelligent design.

    I’ll bet you when James Cook first sailed to Easter island, he knew the Rapa Nui statues were designed right away.

    You sir are no James Cook.

  25. There isn’t anything in DNA that looks “obviously” designed to me. Not even likely designed. Simply put, there’s nothing about DNA as found in living organisms that gives away a hint of anything I would associate with being the product of intelligent design.

    Antony Flew stopped fighting against ID just because of DNA. It may not look designed to the anti-ID mob but they sure as hell don’t have anything capable of explaining the existence of DNA.

    So they can deny all they want. By doing so they prove they are not skeptics as they apply their “skepticism” too selectively.

  26. Frankie,

    I don’t know about that. Can blind and mindless processes produce DNA at all? That still needs to be demonstrated

    Not before you can take a view on junk. Cars are designed, but we still know a non-functioning one when we see one.

  27. Allan Miller:
    Frankie,

    Not before you can take a view on junk. Cars are designed, but we still know a non-functioning one when we see one.

    OK so you don’t have a mechanism capable of producing DNA. Got it.

    My view on junk DNA is we don’t know enough to make that decision. There could be some junk but I know enough to know what Larry says is untestable nonsense- that a human could develop if we removed the right 90% of the genome.

  28. Allan Miller:
    REW,

    ‘Perfected’ bacteria are part of the Fall. No good making Pestilence inefficient!

    Allan,

    Have you ever considered going into Theology? You’d be a natural!!

  29. phoodoo: REW,

    What’s the explanation for pufferfish?

    I havent read anything on this recently but last I remember there wasn’t an explanation. Just an observation that pufferfish have less junk ( and smaller genomes) than other teleost fish. Before you go on to say this supports ID could you at least acknowledge that this is strong evidence that the extra DNA in other fish is in fact ‘junk’?

  30. REW: Before you go on to say this supports ID could you at least acknowledge that this is strong evidence that the extra DNA in other fish is in fact ‘junk’?

    Why would that be so? Because we haven’t figured out the purpose of the other DNA in other fish?

    All we can conclude from the pufferfish is that some animals DON’T have lots of junk DNA. Not that others do.

  31. phoodoo:
    Now, How did James Cook know the statues on Easter Island were designed?

    He didn’t know it was “designed”, he inferred they were conceived and sculpted by people, because he had previous knowledge of people doing exactly that, and because the statues themselves look like people.

    We have none of any such previous knowledge for living things

  32. REW: Before you go on to say this supports ID could you at least acknowledge that this is strong evidence that the extra DNA in other fish is in fact ‘junk’?

    We don’t know enough about it, yet. Just because a programmer can get by with fewer lines of code than another programmer doesn’t mean those extra lines of code are junk.

  33. phoodoo: REW: Before you go on to say this supports ID could you at least acknowledge that this is strong evidence that the extra DNA in other fish is in fact ‘junk’?

    Why would that be so? Because we haven’t figured out the purpose of the other DNA in other fish?

    Well think about this for a while and try to see the logic. I’ll illustrate it without giving the answer away.

    Pufferfish genome- .. ABCDE
    Genomes of many other fish similar in complexity- ABCDEFGHIJK

    Which part is ‘junk’ and why?

  34. dazz: phoodoo:
    Now, How did James Cook know the statues on Easter Island were designed?

    They don’t reproduce.

    They’re relatively simple and rationally composed. While we do make increasingly complex designs, we’ve not reached the complexity of life, nor do we operate according to the limits and constraints of evolution as the processes that produced life do, notably, constraints of heredity.

    Why do archaeologists not mistake the remains of life as intelligently-made artifacts?

    Glen Davidson

  35. REW,

    I havent read anything on this recently but last I remember there wasn’t an explanation.

    A reasonably well supported explanation is that of Michael Lynch – he regards the greater intensity of selection against junk in larger populations to be a primary driver. There is a correlation between population size and junk.

    I think he over-extends it across kingdoms though – there are mechanistic and ecological differences that, I think, are of greater significance than the inevitable increase in population size as organisms get smaller.

  36. Allan Miller says, “… we still know a non-functioning one when we see one.”

    Frankie says,
    My view on junk DNA is we don’t know enough to make that decision.

    YOU don’t know enough to participate in this debate but that doesn’t mean the experts are as ignorant as you. Biochemists have been working with genes/DNA for more than half-a-century. They know how to recognize genes and broken genes.

    There could be some junk but I know enough to know what Larry says is untestable nonsense- that a human could develop if we removed the right 90% of the genome.

    You do not know enough to say that my views are nonsense. And you certainly don’t know enough to say my views are untestable.

  37. Rumraket: One of these rocks is “designed”, in the sense of being a Palaeolithic stone tool fashioned by human hand.

    All your picture needs is a watch and it would be straight out of Paley!

  38. So I am finally reading this book on junk DNA and human evolution. Amazing the things you learn.

    Like the idea that the universe came from nothing is not science. Some judge ruled so. Sorry, atheists. You either agree with the theists that something always existed or you go off to the “not science” camp.

    Also learned that Intelligent Design is not Creationism. Sorry, Patrick.

  39. Larry Moran: You do not know enough to say that my views are nonsense. And you certainly don’t know enough to say my views are untestable.

    Then test them, Larry. Show us that you can remove 90% of the human genome and still get a human to develop. Or admit your idea is untestable nonsense/ wishful thinking.

    Biochemists have been working with genes/DNA for more than half-a-century. They know how to recognize genes and broken genes.

    Biochemists can’t say how DNA arose in the first place. They can’t account for coding DNA. They can’t account for then genetic code. And they definitely can’t say if the alleged junk is actually used as storage for the immaterial instruction sets.

  40. Frankie:
    It’s moronic to say that ID is unfalsifiable after you have been told how to falsify ID.

    It certainly isn’t moronic to believe you are mistaken

    To falsify any given design inference all one has to do is step up and show non-telic processes can account for it.

    Are those the same non-telic processes you claim are untestable? If true, it is impossible to ever prove non design, therefore it is impossible to disprove design.

    Say you are mistaken ,erosion is a non telic process which can be shown to be capable of creating the Grand Canyon. That alone would not falsify design unless one knew something about the designer’s capabilities. You don’t. Therefore design cannot be ruled out

    That even applies to Stonehenge- however no one can. That means the design inference for Stonehenge is unfalsifiable which makes it an incontrovertible fact that it was designed.

    I agree, Trump Tower is also designed.

    isn’t ID’s fault that there isn’t any way for blind and mindless processes to produce what IDists say is designed.

    Then thanks for admitting that without a proposed way to implement the design and designer ,design cannot be falsified. ID is unfalsifiable by design.

  41. Frankie:

    Biochemists can’t say how DNA arose in the first place.

    Neither can ID

    And they definitely can’t say if the alleged junk is actually used as storage for the immaterial instruction sets.

    Neither can ID since ID cannot speak to how the design is implemented

  42. Mung:
    Also learned that Intelligent Design is not Creationism. Sorry, Patrick.

    You might be interested in what Phillip Johnson has to say about this. He is one of the founders of the modern Intelligent Design movement.

    I am not interested in any claims that are based on a literal reading of the Bible, nor do I understand the concept of creation as narrowly as Duane Gish does. If an omnipotent Creator exists He might have created things instantaneously in a single week or through gradual evolution over billions of years. He might have employed means wholly inaccessible to science, or mechanisms that are at least in part understandable through scientific investigation.

    The essential point of creation has nothing to do with the timing or the mechanism the Creator chose to employ, but with the element of design or purpose. In the broadest sense, a “creationist” is simply a person who believes that the world (and especially mankind) was designed and exists for a purpose. With the issue defined that way, the question becomes: Is mainstream science opposed to the possibility that the natural world was designed by a Creator for a purpose? Is so, on what basis?
    Phillip Johnson “Darwin on Trial” (1993)

    I use the same meaning as Phillip Johnson. A creationist is anyone who thinks the world was designed by a creator. The movement he founded is a version of creationism and that’s why we call it Intelligent Design Creationism.

    You are free to use different definitions if you wish but you must respect the definitions used by others.

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